One of the gravest revelations so far made about the missing "paragraph 168" of this week's appeal court judgment in the Binyam Mohamed case is that parliament's intelligence and security committee (ISC) was misled by MI5.

Government lawyer Jonathan Sumption QC, in a letter demanding the deletion of paragraph 168, confirmed this, pointing out that the judgment stated: "Officials of the service deliberately misled the ISC." He was referring to evidence given to a secret session of the ISC on 23 November 2006 by the then head of MI5, Eliza Manningham-Buller. She was testifying about events in May 2002 that took place under her predecessor, Stephen Lander.

According to the ISC's later heavily redacted report, Manningham-Buller and her team denied all knowledge of Mohamed's ill-treatment. The committee – chaired by the former Northern Ireland secretary Paul Murphy – was told: "A member of the security service did interview [Mohamed] once for a period of approximately three hours while he was detained in Karachi in 2002." The interrogator, later known as Witness B, was "an experienced officer" who conducted the interview "in line with the services' guidance to staff on contact with detainees".

The ISC recorded: "The security service denies that the officer told [Mohamed] he would be tortured as he alleges … He did not observe any abuse and … no instances of abuse were mentioned by [Mohamed]."

Murphy's committee duly reassured the public that although MI5 conceded they had not demanded specific assurances from the US that Mohamed was being properly treated: "This is understandable given the lack of knowledge at the time of any possible consequences of US custody of detainees."

That part of the published ISC report now appears to have been untrue. The judges found that MI5 had 42 documents, detailing how both Witness B and "persons senior to Witness B" had been briefed in detail at the time about how the US was deliberately ill-treating Mohamed as part of a "new strategy", systematically depriving him of sleep, terrifying him with threats of rendition and shackling him in interrogations.

But the courts did not accuse Manningham-Buller personally of deceit, ruling earlier that although the existence of the 42 files had been withheld from the ISC: "The evidence was that earlier searches made had not discovered them."

Witness B is being investigated by the Metropolitan police for "possible criminal wrongdoing", the government says.